Driving molecular assembly into micrometer-scale patterns is key for defining advanced materials of interest in various fields, including life sciences, photovoltaics, and quantum photonics. However, the driving process competes with other forces, such as Brownian motion, ripening phenomena, capillary forces, and non-specific adsorption. Here we report on a guided diffusion mechanism of luminescent dye molecules encapsulated inside boron nitride nanotubes (BNNTs). Correlative measurements between BNNT bending and molecular position along the BNNT axis reveal an efficient and long-range migration of dyes from curved to straight regions of the nanotube. This curvature activated diffusion forms clusters of bright J-aggregates in periodic patterns of well-defined spacing and length. A phenomenological model of guided molecular transport in bended BNNTs is used to describe this directed 1D diffusion inside BNNT. It is shown to accurately predict the position and morphologies of a J-aggregate as a function of nanotube length. Coupling topological stimuli to 1D molecular diffusion at the nanoscale is here presented as an interesting tool capable of reconfiguring various emissive patterns of functional molecules at the mesoscopic scale.